Abstract

Negative regulatory elements (NREs) are deoxyribonucleic acid (DNA) sequences that repress gene expression. NREs can act locally
to repress expression of individual genes, or globally to repress expression of an expansive chromosomal domain. In either
case, NREs act as binding sites for specific proteins, which in turn interact with other factors either to block recruitment
of ribonucleic acid (RNA) polymerase or to facilitate formation of heterochromatin.

Keywords: chromatin; repression; silencing; transcription

Figure 1.

Schematic summary of a eukaryotic RNAP II promoter. Repressor and activator proteins are depicted as bipartite structures: one domain binds the cognate DNA sequence, either the NRE (URS) or positive regulatory element (UAS or enhancer), and the other domain interacts with components of the transcription machinery. Some repressors and activators
interact directly with the core transcriptional machinery, including the general transcription factors (GTFs) or RNAP II itself, whereas others exert their effects through corepressor or coactivator complexes. These cofactors can
in turn interact with the core machinery, as depicted here, or affect chromatin structure (Malave and Dent, ). The relative position of the URS and UAS elements depicted here is arbitrary.

Figure 2.

Schematic summary of the structure of SIR‐mediated silent DNA. Like URS elements, silencers function as binding sites for sequence‐specific DNA‐binding proteins (a, b, c), which in turn bind SIR proteins to turn off gene expression. In contrast to NREs that repress local gene expression, silencers repress an expansive chromosomal domain. The silencer serves as a nucleation
site for spreading the SIR complex along adjacent nucleosomes (N) (Rusche et al., ). This structure is comparable to the heterochromatin of higher eukaryotes.

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